Dr. Hai Fang Prof. Gough's Research Group Department of Computer Science University of Bristol The Merchant Venturers Building Woodland Road Bristol BS8 1UB, United Kingdom Email: hfang@cs.bris.ac.uk

Academic Records

• Post-Doctoral Research Associate (2010 - Now) in Intelligent Systems Laboratory, Department of Computer Science, University of Bristol
• Research postDoc (2009 - 2010) from Sino-French Laboratory of Genomics and Life Sciences, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine
• M.S. - Ph.D. program in Genetics/Bioinformatics/Systems Biology (2003 - 2009) from Institute of Health Sciences, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences
• B.S. in Biotechnology Engineering (1999 - 2003) from Jiangnan University

Interests and Projects

• Large-scale epigenomic data mining
• Evolution of protein domain networks
• Species/sequenced tree of life (sTOL)
• The dcGO database of domain-centric ontologies
• Function and phenotype prediction for genome sequences (dcGO Predictor) and domain sets (dcGO Enrichment)
• Network-oriented connections among diseases, drugs and phenotypes using Random Walk with Restart
• Topology-preserving selection and clustering of bio-omics data (i.g., transcriptome) using Self-Organizing Map

Academic Publications

• Fang H, Gough J. (2013) A disease-drug-phenotype matrix inferred by walking on a functional domain network. Molecular BioSystems PubMed ID:(23462907) PDF
• Fang H, Gough J. (2013) A domain-centric solution to functional genomics via dcGO Predictor. BMC Bioinformatics 14(Suppl 3):S9 (In Press) PDF
• Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Toronen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kassner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Honigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Bjorne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Skunca N, Supek F, Bosnjak M, Panov P, Dzeroski S, Smuc T, Kourmpetis YA, van Dijk AD, Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I. (2013) A large-scale evaluation of computational protein function prediction. Nature Methods 10(3):221-7 PubMed ID:(23353650) PDF
• Fang H, Gough J. (2012) dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. Nucleic Acids Res 41(Database issue):D536-44 PubMed ID:(23161684) PDF
• de Lima Morais DA, Fang H*, Rackham OJ, Wilson D, Pethica R, Chothia C, Gough J. (2011) SUPERFAMILY 1.75 including a domain-centric gene ontology method. Nucleic Acids Res 39 (Database issue), D427-34 PubMed ID:(21062816) PDF
• Fang H, Du Y, Xia L, Li J, Zhang J, Wang K. (2011) A topology-preserving approach for selection and clustering of multi-dimensional biological data. OMICS: A Journal of Integrative Biology 15 (7-8), 483-94 PubMed ID:(21699401) PDF
• Fang H, Yang Y, Li CL, Fu S, Yang Z, Jin G, Wang K, Zhang J, Jin Y. (2010) Transcriptome Analysis of Early Organogenesis in Human Embryos. Developmental Cell 19 (1), 174-184 PubMed ID:(20643359) PDF. This work is highlighted by Genome Biology (Elucidating the molecular characteristics of organogenesis in human embryos), and followed up by BMC Systems Biology
• Liu R, Wang W, Ye L, Bi Y, Fang H, Cui B, Zhou W, Dai M, Zhang J, Li X, Ning G. (2010) p21-Activated kinase 3 is overexpressed in thymic neuroendocrine tumors (carcinoids) with ectopic ACTH syndrome and participates in cell migration. Endocrine 38 (1), 38-47 PubMed ID:(20960100) PDF
• Wang K, Wang P, Shi J, Zhu X, He M, Jia X, Yang X, Qiu F, Jin W, Qian M, Fang H, Mi J, Yang X, Xiao H, Minden M, Du Y, Chen Z, Zhang J. (2010) PML/RARalpha Targets Promoter Regions Containing PU.1 Consensus and RARE Half Sites in Acute Promyelocytic Leukemia. Cancer Cell 17 (2), 186-197 PubMed ID:(20159610) PDF
• Bi Y, Liu R, Ye L, Fang H, Li X, Wang W, Zhang J, Wang K, Jiang L, Su T, Chen Z, Ning G. (2009) Gene expression profiles of thymic neuroendocrine tumors (carcinoids) with ectopic ACTH syndrome reveal novel molecular mechanism. Endocrine-Related Cancer 16 (4), 1273-82 PubMed ID:(19625467) PDF
• Fang H, Zhang J and Wang K. (2009) Connecting biological themes using a single human network of gene associations. International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing 463 - 471 (IJCBS) PDF
• Fang H. Systems for In-depth Mining of BioX-omic data (SimBioX). PhD Thesis (Supervised by Zhang J), Spring 2009
• Wang K, Fang H*, Xiao D, Zhu X, He M, Pan X, Shi J, Zhang H, Jia X, Du Y, Zhang J. (2009) Converting Redox Signaling to Apoptotic Activities by Stress-Responsive Regulators HSF1 and NRF2 in Fenretinide Treated Cancer Cells. PLoS ONE 4 (10), e7538 PubMed ID:(19844581) PDF
• Fang H, Wang K, Zhang J. (2008) Transcriptome and proteome analyses of drug interactions with natural products. Current Drug Metabolism 9 (10), 1038-48 PubMed ID:(19075620) PDF
• Du Y, Wang K, Fang H, Li J, Xiao D, Zheng P, Chen Y, Fan H, Pan X, Zhao C, Zhang Q, Imbeaud S, Graudens E, Eveno E, Auffray C, Chen S, Chen Z, Zhang J. (2006) Coordination of intrinsic, extrinsic, and endoplasmic reticulum-mediated apoptosis by imatinib mesylate combined with arsenic trioxide in chronic myeloid leukemia. Blood 107 (4), 1582-90 PubMed ID:(16249384) PDF